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- PDB-1ju3: BACTERIAL COCAINE ESTERASE COMPLEX WITH TRANSITION STATE ANALOG -

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Basic information

Entry
Database: PDB / ID: 1ju3
TitleBACTERIAL COCAINE ESTERASE COMPLEX WITH TRANSITION STATE ANALOG
Componentscocaine esterase
KeywordsHYDROLASE / alpha/beta hydrolase
Function / homology
Function and homology information


cocaine esterase / cocaine catabolic process / dipeptidyl-peptidase activity / carboxylic ester hydrolase activity / cytoplasm
Similarity search - Function
alpha-amino acid ester hydrolase ( Helical cap domain) / alpha-amino acid ester hydrolase ( Helical cap domain) / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / : / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Galactose-binding domain-like ...alpha-amino acid ester hydrolase ( Helical cap domain) / alpha-amino acid ester hydrolase ( Helical cap domain) / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / : / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Jelly Rolls / Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHENYL BORONIC ACID / Cocaine esterase
Similarity search - Component
Biological speciesRhodococcus sp. MB1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsLarsen, N.A. / Turner, J.M. / Stevens, J. / Rosser, S.J. / Basran, A. / Lerner, R.A. / Bruce, N.C. / Wilson, I.A.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Crystal structure of a bacterial cocaine esterase.
Authors: Larsen, N.A. / Turner, J.M. / Stevens, J. / Rosser, S.J. / Basran, A. / Lerner, R.A. / Bruce, N.C. / Wilson, I.A.
History
DepositionAug 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cocaine esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4742
Polymers63,3521
Non-polymers1221
Water9,800544
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.08, 106.08, 221.52
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein cocaine esterase


Mass: 63351.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. MB1 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L9D7
#2: Chemical ChemComp-PBC / PHENYL BORONIC ACID


Mass: 121.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7BO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10mM DTT, 10mM Tris pH 7.5, 25 mM NaCl, 1.6 M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 22.5K
Crystal
*PLUS
Density % sol: 53 %
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris11pH7.5
225 mM11NaCl
310 mMdithiothreitol11
440 mg/mlprotein11
51.5-1.8 Mammonium sulfate12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11201
21201
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.965
SYNCHROTRONSSRL BL11-120.965
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMar 7, 2001
ADSC QUANTUM 42CCDMar 7, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.58→20 Å / Num. all: 90349 / Num. obs: 90349 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.064
Reflection shellResolution: 1.58→1.61 Å / Rmerge(I) obs: 0.514 / % possible all: 71.2
Reflection
*PLUS
Lowest resolution: 20 Å / Redundancy: 5.4 %
Reflection shell
*PLUS
% possible obs: 71.2 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JU4, cocE enzyme

1ju4


Resolution: 1.58→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.214 4517 Random
Rwork0.199 --
all0.199 90349 -
obs0.199 90349 -
Refine analyzeLuzzati coordinate error obs: 0.1881 Å / Luzzati d res low obs: 20 Å / Luzzati sigma a obs: 0.1312 Å
Refinement stepCycle: LAST / Resolution: 1.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4351 0 9 544 4904
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d1.6
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.6

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